Variant report

Variant	rs4803801
Chromosome Location	chr19:38626108-38626109
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38625391..38627747-chr19:38633636..38636533,2	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10403716	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10405667	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10412762	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10412865	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10413751	0.81[JPT][hapmap]
rs10420506	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10422665	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1568975	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1614979	0.87[CEU][hapmap];0.83[CHB][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1622409	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1625884	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1654349	0.81[JPT][hapmap]
rs1654355	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1654357	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1654358	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1654359	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1654365	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1654367	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1725461	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1725473	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1725475	0.81[JPT][hapmap]
rs1725479	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1725512	0.87[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2005054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2010234	0.86[YRI][hapmap]
rs2082442	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2082443	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28412601	0.86[AMR][1000 genomes]
rs28581256	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3760882	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3810356	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4802233	0.87[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4802239	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4802247	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4802256	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4802278	0.81[CEU][hapmap];0.81[CHB][hapmap]
rs4803786	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4803800	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4803802	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4803803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4803810	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4803828	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4803829	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4803862	0.81[CEU][hapmap];0.81[CHB][hapmap]
rs56166457	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58152231	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59185302	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59579475	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59924887	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61388128	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs705505	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71179415	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7248428	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7250034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs729625	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs729626	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs735615	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs754123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8105468	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8106266	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs855601	0.81[JPT][hapmap]
rs855603	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs855619	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs855621	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs855623	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs855624	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs855625	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs855627	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs855630	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs855631	0.81[EUR][1000 genomes]
rs855633	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs855634	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs855636	0.81[JPT][hapmap]
rs855637	0.81[JPT][hapmap]
rs855638	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs855640	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs855641	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs860623	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs863020	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs941039	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs941040	0.87[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9941456	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9941467	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4803801	DPF1	cis	Skin Sun Exposed Lower leg	GTEx
rs4803801	BCAM	cis	parietal	SCAN
rs4803801	SIPA1L3	cis	Heart Left Ventricle	GTEx
rs4803801	CCDC8	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38591800-38642800	Weak transcription	Small Intestine	intestine
2	chr19:38600600-38652800	Weak transcription	NHDF-Ad	bronchial
3	chr19:38610800-38643600	Weak transcription	HepG2	liver
4	chr19:38611000-38652800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:38611600-38634400	Weak transcription	Stomach Mucosa	stomach
6	chr19:38611600-38634800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr19:38611600-38634800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr19:38611600-38641400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr19:38611600-38653000	Weak transcription	HUVEC	blood vessel
10	chr19:38611800-38634600	Weak transcription	NH-A	brain
11	chr19:38611800-38642600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr19:38611800-38653000	Weak transcription	Fetal Kidney	kidney
13	chr19:38613400-38633600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:38613400-38634400	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr19:38613600-38634800	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr19:38613800-38629800	Weak transcription	Liver	Liver
17	chr19:38613800-38630000	Weak transcription	Brain Hippocampus Middle	brain
18	chr19:38613800-38633000	Weak transcription	Brain Angular Gyrus	brain
19	chr19:38613800-38633000	Weak transcription	Brain Substantia Nigra	brain
20	chr19:38613800-38633400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr19:38613800-38635600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr19:38613800-38636600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr19:38613800-38639000	Weak transcription	Left Ventricle	heart
24	chr19:38613800-38641800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr19:38613800-38643200	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr19:38613800-38652200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr19:38613800-38652600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr19:38614000-38630200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr19:38614000-38634800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr19:38616000-38652600	Strong transcription	Primary B cells from peripheral blood	blood
31	chr19:38616200-38641600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr19:38616600-38642000	Weak transcription	Dnd41	blood
33	chr19:38617000-38652000	Strong transcription	Fetal Intestine Small	intestine
34	chr19:38617800-38626400	Strong transcription	Osteobl	bone
35	chr19:38618200-38651000	Strong transcription	Fetal Intestine Large	intestine
36	chr19:38618400-38626600	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr19:38619000-38626600	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr19:38619000-38630800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr19:38619600-38647800	Strong transcription	Fetal Stomach	stomach
40	chr19:38620600-38626800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr19:38620800-38626200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr19:38620800-38626800	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr19:38620800-38632600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr19:38621000-38627000	Strong transcription	Duodenum Mucosa	Duodenum
45	chr19:38621000-38633800	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr19:38621400-38629000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr19:38621600-38630400	Weak transcription	Ovary	ovary
48	chr19:38621600-38642800	Weak transcription	NHLF	lung
49	chr19:38621800-38634000	Weak transcription	Thymus	Thymus
50	chr19:38622000-38634600	Weak transcription	Brain Germinal Matrix	brain

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